Long-term warming modulates diversity, vertical structuring of microbial communities, and sulfate reduction in coastal Baltic Sea sediments

Abstract

Coastal waters such as those found in the Baltic Sea already suffer from anthropogenic related problems including increased algal blooming and hypoxia while ongoing and future climate change will likely worsen these effects. Microbial communities in sediments play a crucial role in the marine energy- and nutrient cycling, and how they are affected by climate change and shape the environment in the future is of great interest. The aims of this study were to investigate potential effects of prolonged warming on microbial community composition and nutrient cycling including sulfate reduction in surface (∼0.5 cm) to deeper sediments (∼ 24 cm). To investigate this, 16S rRNA gene amplicon sequencing was performed, and sulfate concentrations were measured and compared between sediments in a heated bay (which has been used as a cooling water outlet from a nearby nuclear power plant for approximately 50 years) and a nearby but unaffected control bay. The results showed variation in overall microbial diversity according to sediment depth and higher sulfate flux in the heated bay compared to the control bay. A difference in vertical community structure reflected increased relative abundances of sulfur oxidizing- and sulfate reducing bacteria along with a higher proportion of archaea, such as Bathyarchaeota, in the heated compared to the control bay. This was particularly evident closer to the sediment surface, indicating a compression of geochemical zones in the heated bay. These results corroborate findings in previous studies and additionally point to an amplified effect of prolonged warming deeper in the sediment, which could result in elevated concentrations of toxic compounds and greenhouse gases closer to the sediment surface.

Keywords: 16S rRNA gene amplicon; climate change; depth profile; microbial communities; sediments.

FIGURE 1

Sulfate concentrations; mean (n = 3) ± s.d. sulfate concentration in the heated and control bays at the three different depths. Sulfate fluxes for each bay were calculated based on average temperature measured in each bay and assumed salinity of 6 psu and sediment porosity of 0.8 (within the range of uncompacted mud).

FIGURE 2

Non-metric multidimensional scaling (nMDS) of the samples within the heated (orange) and control (blue) bays at the three different sediment depths.

FIGURE 3

Relative abundances of bacteria and archaea from the two bays at the three sediment sampling depths showing the surface (outer circle), middle (middle circle), and deep (inner circle) communities (A) along with stacked bar graphs of bacteria (B) with >1% relative abundance and archaea (C) on the class level for the different sampling depths in the two bays.

FIGURE 4

Significant differential abundant families with relative abundance above 1% and a log₂ fold change of at least two within the heated and control bay at the three different depths (A) and venn diagrams of the significant ASVs within the heated and control bays at the three sediment depths (B).

FIGURE 5

16S rRNA gene ASV based prediction of sulfur cycling related functional abundances. Bray–Curtis based db-RDA of predicted functional genes related with sulfur cycling according to KEGG identifiers for the heated (triangle) and control (circle) bays at surface (purple), middle (green), and deep (red) sediment depths with the environmental parameters of sulfate and temperature (A) along with plots of relative abundances of selected dissimilatory sulfate reduction and sulfide oxidation genes in the control (left) and heated (right) bay (B).